results {FRASER}R Documentation

Extracting results and aberrant splicing events

Description

The result function extracts the results from the given analysis object based on the given options and cutoffs. The aberrant function extracts aberrant splicing events based on the given cutoffs.

Usage

results(x, ...)

## S4 method for signature 'FraserDataSet'
results(
  x,
  sampleIDs = samples(x),
  padjCutoff = 0.05,
  zScoreCutoff = NA,
  deltaPsiCutoff = 0.3,
  minCount = 5,
  psiType = c("psi3", "psi5", "psiSite"),
  additionalColumns = NULL,
  BPPARAM = bpparam()
)

resultsByGenes(res, geneColumn = "hgncSymbol", method = "BY")

aberrant(
  fds,
  type = currentType(fds),
  padjCutoff = 0.05,
  deltaPsiCutoff = 0.3,
  zScoreCutoff = NA,
  minCount = 5,
  by = c("none", "sample", "feature"),
  aggregate = FALSE,
  ...
)

Arguments

x, fds

FraserDataSet

...

Further arguments can be passed to the method. If "zscores", "padjVals" or "dPsi" is given, the values of those arguments are used to define the aberrant events.

sampleIDs

A vector of sample IDs for which results should be retrieved

padjCutoff

The FDR cutoff to be applied or NA if not requested.

zScoreCutoff

The z-score cutoff to be applied or NA if not requested.

deltaPsiCutoff

The cutoff on delta psi or NA if not requested.

minCount

The minimum count value of the total coverage of an intron to be considered as significant. result

psiType

The psi types for which the results should be retrieved.

additionalColumns

Character vector containing the names of additional columns from mcols(fds) that should appear in the result table (e.g. ensembl_gene_id). Default is NULL, so no additional columns are included.

BPPARAM

The BiocParallel parameter.

res

Result as created with results()

geneColumn

The name of the column in mcols(res) that contains the gene symbols.

method

The p.adjust method that is being used to adjust p values per sample.

type

Splicing type (psi5, psi3 or psiSite)

by

By default none which means no grouping. But if sample or feature is specified the sum by sample or feature is returned

aggregate

If TRUE the returned object is based on the grouped features

Value

GRanges object

For results: GRanges object containing significant results. For aberrant: Either a of logical values of size introns/genes x samples if "by" is NA or a vector with the number of aberrant events per sample or feature depending on the vaule of "by"

Examples

# get data, fit and compute p-values and z-scores
fds <- createTestFraserDataSet()

# extract results: for this example dataset, z score cutoff of 2 is used to
# get at least one result and show the output
res <- results(fds, padjCutoff=NA, zScoreCutoff=3, deltaPsiCutoff=0.05)
res

# aggregate the results by genes (gene symbols need to be annotated first 
# using annotateRanges() function)
resultsByGenes(res)

# get aberrant events per sample: on the example data, nothing is aberrant
# based on the adjusted p-value
aberrant(fds, type="psi5", by="sample")

# get aberrant events per gene (first annotate gene symbols)
fds <- annotateRangesWithTxDb(fds)
aberrant(fds, type="psi5", by="feature", zScoreCutoff=2, padjCutoff=NA,
        aggregate=TRUE)
        
# find aberrant junctions/splice sites
aberrant(fds, type="psi5")

[Package FRASER version 1.0.2 Index]